Nyemtaay is a python library for population genetics caluclations.
The name nyemtaay
is from a Kumeyaay (Ipai) word for "cougar", in homage to the inigenous peole of Southern California, on whose land we live and wok.
Nyemtaay runs under python3 (>3.9)
We recommend that you install directly from the main GitHub repository using pip (which works with an Anaconda environment as well):
$ python3 -m pip install --user --upgrade git+https://github.com/aortizsax/nyemtaay.git
Below I will outline the applications icluding traditional popgen stats, information theory analysis, and tissue of origin for a cancer dataset.
Once cloned locally, check the help page
nyemtaay -h
The greek bears data will be used to show the functionality of Nyemtaay.
cd nyemtaay/tests/testdata/greekbears
nyemtaay -f bear_aln_sequences.fasta -m metadata_lat_long.csv -s LOC -calc norm-jsd -dm
nyemtaay -f bear_aln_sequences.fasta -m metadata_lat_long.csv -s LOC -calc directionality -dm
nyemtaay -f bear_aln_sequences.fasta -m metadata_lat_long.csv -s LOC -calc norm-jsd-cluster -dm
nyemtaay -f bear_aln_sequences.fasta -m metadata_lat_long.csv -s LOC -calc directionality norm-jsd-cluster -dm
nyemtaay -f bear_aln_sequences.fasta -m metadata_lat_long.csv -s LOC -calc nei-fst